MolNFT v2 · #111299 · protein
TcdA (CsdL)
4YED · tRNA threonylcarbamoyladenosine dehydratase: “TcdA (CsdL)”. X-ray diffraction at 1.9, 1 ligand (AMP), 13 pockets (best druggability 0.80). MolNFT v2 #111299 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YED
- Type
- protein
- Length
- 1,006 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Escherichia coli K12
- Molecule
- tRNA threonylcarbamoyladenosine dehydratase
- EC
- 6.1.-.-
- UniProt
- Q46927
- Ligands
- AMP
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.9 · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | tRNA threonylcarbamoyladenosine dehydratase (EC 6.1.-.-) | protein | 245 | 47% helix, 14% strand | Q46927 |
| B | tRNA threonylcarbamoyladenosine dehydratase (EC 6.1.-.-) | protein | 254 | 45% helix, 17% strand | Q46927 |
| C | tRNA threonylcarbamoyladenosine dehydratase (EC 6.1.-.-) | protein | 252 | 45% helix, 16% strand | Q46927 |
| D | tRNA threonylcarbamoyladenosine dehydratase (EC 6.1.-.-) | protein | 255 | 44% helix, 16% strand | Q46927 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.80 | 0.81 | 95 | empty |
| 2 | 339 | 0.65 | 0.80 | 50 | AMP |
| 3 | 365 | 0.64 | 0.79 | 49 | AMP |
| 4 | 338 | 0.63 | 0.79 | 43 | AMP |
| 5 | 314 | 0.62 | 0.79 | 43 | AMP |
Interfaces
5 interfaces between chains.
- A–B · 2418 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2356 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 464 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 227 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 114 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q46927
- Elsewhere: RCSB PDB 4YED · PDBe 4YED · UniProt Q46927
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